Now that you mention it, I do recall being able to walk into the hotel room -- you just couldn't rest unless you talked to the receptionist. I believe I was consciously walking upstairs to end the day for the first (5?) chapters I played in succession, but the instinct slipped my mind due to taking a break for a few weeks. I think I even had a false memory of Lianna saying "I have to talk to the receptionist first" after going to "normal" inns in other towns where going upstairs triggered a "you have to pay a room first" message. I agree having Lianna say it's time to go upstairs would probably be the best way to resolve this. It is always surprising just how often the hardest "glitch" to avoid is actually human players just not understanding what they are supposed to do...
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Now things suddenly got really deep xD
Since Lianna already owns a room in Eastwall's inn, the ones in Mappi Village are the only ones that give you a message when you try going upstairs, so maybe that's where your memory comes from.
I know it's kinda weird having to pay to get the heal in Eastwall when Lianna already has a room, but I made it that way so players don't feel the need to walk all the way back from anywhere just to get a free heal (I know I'd do it lol). But we can just imagine we're paying for another room for Jeanne and Mao instead, since Lianna's only has one bed.
I get completely why you set up the system so that you have to pay when you have your party with you -- and you bet I go out of my way to travel to free sleeping locations too. I remember at least one game in which they eventually gave you a world map where you could travel to any location and I basically never paid for an inn again :)
Had not realized just how philosophical my comment got over some simple inn options XD.